From owner-chemistry@ccl.net Sun Jan 13 04:22:01 2013 From: "Val Gillet v.gillet-$-sheffield.ac.uk" To: CCL Subject: CCL: CFP for the Sixth Joint Sheffield Conference on Chemoinformatics Message-Id: <-48059-130113041306-17325-i8jMrYjTsk0+0klqhf6rpA-#-server.ccl.net> X-Original-From: "Val Gillet" Date: Sun, 13 Jan 2013 04:13:05 -0500 Sent to CCL by: "Val Gillet" [v.gillet]![sheffield.ac.uk] Sixth Joint Sheffield Conference on Chemoinformatics: Call for Papers University of Sheffield, 22nd-24th July 2013 (http://cisrg.shef.ac.uk/shef2013/) The Chemical Structure Association Trust and the Molecular Graphics and Modelling Society announce their Sixth Joint Sheffield Conference on Chemoinformatics. The conference will be held at the University of Sheffield, UK. Offers of papers are welcomed on new developments in all aspects of chemoinformatics. Possible topics include (but are not limited to): * Virtual Screening, e.g., docking and pharmacophore analysis, similarity and clustering methods, machine learning * Computational methods for lead identification and optimisation, e.g., modelling and structure-activity methods. ADMET prediction, de novo design * High-throughput screening, e.g., assay quality control, design of screening collections, systems based design * New algorithms and technologies, e.g., data mining, distributed processing, cloud computing, open source chemoinformatics software, visualisation * Emerging applications, e.g., linking biological and chemical data, SAR transfer between series, target drugability, the Semantic Web, text mining * Case histories, incorporating practical experience of any of the above The programme will have space for ca. two dozen oral presentations, and there will also be extensive opportunities for poster presentations. Authors wishing to submit a paper should complete the template provided at http://cisrg.shef.ac.uk/shef2013/abstract_submission.php, stating whether they wish to be considered for oral or for poster presentation. Abstracts should be 500-750 words in length. The deadline for abstract submission is 25th January 2013. Submissions will be selected for oral or poster presentation by the Programme Committee, with notification of acceptance by 28th February 2013. In selecting papers for oral presentation, the Committee will seek to achieve a balance between the various areas of the subject and between new methodologies and successful applications of existing techniques. Further details of the conference, including registration information and opportunities for sponsorship and participation in the conference exhibition will be posted at the conference website http://cisrg.shef.ac.uk/shef2013/ From owner-chemistry@ccl.net Sun Jan 13 10:07:00 2013 From: "Dr. Lars Goerigk lars.goerigk]*[chem.usyd.edu.au" To: CCL Subject: CCL:G: Unexpected error in G09 Rev B.01 Message-Id: <-48060-130112174310-21182-XE9JAWaPxR/RScLgsZTP2g+*+server.ccl.net> X-Original-From: "Dr. Lars Goerigk" Content-Type: multipart/alternative; boundary="------------080900000509090703050502" Date: Sun, 13 Jan 2013 09:42:42 +1100 MIME-Version: 1.0 Sent to CCL by: "Dr. Lars Goerigk" [lars.goerigk[#]chem.usyd.edu.au] This is a multi-part message in MIME format. --------------080900000509090703050502 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Sam and Massimo, just a comment to Sam's comment. Using CIS for DFT does make sense and several programs also allow to do that. Then one usually speaks of TDA-DFT, where TDA stands for the Tamm-Dancoff approximation. From another point of view, if you take the RPA equation (TD-HF) and evoke TDA, then the resulting equation is the CIS equation. As linear response TD-DFT is very similar to the TD-HF equations, you can do the same for TD-DFT and get TDA-DFT and I assume that is what Massimo wanted to do when he tried to evoke CIS/B3LYP. However, I am not sure whether Gaussian allows it. I know that NWCHEM and ORCA allow to do TDA-DFT. Excitation energies are very similar to those of full linear response TD-DFT, at a lower computational cost. Transition dipole moments were reported to be more effected by this approximation, however. I hope this could help. Cheers, Lars -- Dr. Lars Goerigk School of Chemistry (Building F11) The University of Sydney, NSW 2006 Australia Profile: http://www.researchgate.net/profile/Lars_Goerigk List of publications: www.researcherid.com/rid/D-3717-2009 --------------080900000509090703050502 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Sam and Massimo,

just a comment to Sam's comment. Using CIS for DFT does make sense and several programs also allow to do that. Then one usually speaks of TDA-DFT, where TDA stands for the Tamm-Dancoff approximation. From another point of view, if you take the RPA equation (TD-HF) and evoke TDA, then the resulting equation is the CIS equation. As linear response TD-DFT is very similar to the TD-HF equations, you can do the same for TD-DFT and get TDA-DFT and I assume that is what Massimo wanted to do when he tried to evoke CIS/B3LYP.

However, I am not sure whether Gaussian allows it. I know that NWCHEM and ORCA allow to do TDA-DFT. Excitation energies are very similar to those of full linear response TD-DFT, at a lower computational cost. Transition dipole moments were reported to be more effected by this approximation, however.

I hope this could help.

Cheers,
Lars
--
Dr. Lars Goerigk
School of Chemistry (Building F11)
The University of Sydney, NSW 2006
Australia
Profile: http://www.researchgate.net/profile/Lars_Goerigk
List of publications: www.researcherid.com/rid/D-3717-2009
--------------080900000509090703050502-- From owner-chemistry@ccl.net Sun Jan 13 12:16:00 2013 From: "Tymofii Nikolaienko tim_mail%x%ukr.net" To: CCL Subject: CCL: proper RI-JK citation Message-Id: <-48061-130113114948-14055-K6On1L9veuAbMNKbMh3bNw[-]server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Sun, 13 Jan 2013 18:49:33 +0200 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail*|*ukr.net] Dear CCLers! Could someone kindly help me and provide proper citation for the paper introducing the "RI-JK" resolution-of-identity algorithm in the form as it is implemented in Orca 2.9 ? My own findings are: a) F. Weigend, Phys. Chem. Chem. Phys. 4, 4285 (2002), b) Neese F., J. Comp. Chem., 24, 1740–1747 (2003), c) S. Kossmann and F. Neese, Chem. Phys. Lett. 481, 240 (2009), but I'm not sure that any of these papers describe _exactly_ the algorithm used in Orca. Thank you in advance! Yours sincerely Tymofii From owner-chemistry@ccl.net Sun Jan 13 20:50:01 2013 From: "Raphael Martinez raphaelmartinez1983(-)gmail.com" To: CCL Subject: CCL:G: CPHF failed to converge in LinEq1 Message-Id: <-48062-130113204930-27498-nUbWYbG+otBbgDgCvY8d+A#server.ccl.net> X-Original-From: "Raphael Martinez" Date: Sun, 13 Jan 2013 20:49:29 -0500 Sent to CCL by: "Raphael Martinez" [raphaelmartinez1983+*+gmail.com] I have this unexpected error using gaussian 09 while trying to optimized a molecule that contains benzene rings conjugated through vinyl groups (0 1). CPHF failed to converge in LinEq1. Error termination via Lnk1e in /soft/gaussian/g09.c01/g09/linda-exe/l508.exel Any ideas how to fix this? Here is the command line of my input, # opt=calcfc m062x/6-311+g(d,p) SCF=(qc,MaxCycle=4100) The reason for the qc, and maxcycle=4100 is because the calculation was failing with a Convergence failure -- run terminated.Error termination via Lnk1e in .../g09/l502.exe. So I have to go extreme and type qc and 4100 max cycles. It is also worth to mention that I was able to run the optimization with out the "+". Thanks a lot for the help From owner-chemistry@ccl.net Sun Jan 13 23:15:00 2013 From: "Neese, Frank frank.neese^cec.mpg.de" To: CCL Subject: CCL: proper RI-JK citation Message-Id: <-48063-130113152610-24213-CZNnVtlkZD1Nqvt/rGGAqQ ~ server.ccl.net> X-Original-From: "Neese, Frank" Content-Language: de-DE Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Sun, 13 Jan 2013 20:25:56 +0000 MIME-Version: 1.0 Sent to CCL by: "Neese, Frank" [frank.neese|-|cec.mpg.de] Dear Timofii, The earliest paper I know that does the Hartree-Fock exchange with RI is by Kendall and Früchtl but I do not recall where it was published. It must have been around the mid/end 1990s. I have investigated the subject in 2000 and the results are in my habilitation thesis from 2001 but never appeared in the literature. The 2003 paper that you mentioned has nothing on the exchange part and hence is only on J, not on K. The Weigend paper was excellent and probably the first to demonstrate efficiency. Our later paper from 2009, while being based on the earlier work, did practically the same as Weigend and we take no credit for origrinality. The scope of the paper was different. If you, however, want to specifically reference the Orca implementation, this is a correct reference. All the best, Sincerely yours, Frank Neese Am 13.01.2013 um 19:59 schrieb "Tymofii Nikolaienko tim_mail%x%ukr.net" : > > Sent to CCL by: Tymofii Nikolaienko [tim_mail*|*ukr.net] > Dear CCLers! > > Could someone kindly help me and provide proper citation for the paper introducing > the "RI-JK" resolution-of-identity algorithm in the form as it is implemented in Orca 2.9 ? > > My own findings are: > a) F. Weigend, Phys. Chem. Chem. Phys. 4, 4285 (2002), > b) Neese F., J. Comp. Chem., 24, 1740–1747 (2003), > c) S. Kossmann and F. Neese, Chem. Phys. Lett. 481, 240 (2009), > but I'm not sure that any of these papers describe _exactly_ the algorithm used in Orca. > > Thank you in advance! > > Yours sincerely > Tymofiihttp://www.ccl.net/chemistry/sub_unsub.shtml> >